Fast force field-based optimization of protein-ligand complexes with graphics processor

MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions

(2011) Andreas Spitzmüller et al.   Journal of Chemical Information and Modeling

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking*

(2011) Simon Leis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Optimization Methods for Virtual Screening on Novel Computational Architectures

(2010) Horacio Perez-Sanchez et al.   Current Computer-Aided Drug Design

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Automated Docking of Flexible Molecules Into Receptor Binding Sites by Ligand Self-Organization In Situ

(2010) Alexander Klenner et al.   Molecular Informatics

Elastic Potential Grids: Accurate and Efficient Representation of Intermolecular Interactions for Fully Flexible Docking

(2009) Sina Kazemi et al.   ChemMedChem

Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds

(2009) Jochen Schlosser et al.   Journal of Chemical Information and Modeling

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

(2008) Tania Pencheva et al.   BMC BIOINFORMATICS

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Harvesting graphics power for MD simulations

(2008) J.A. van Meel et al.   MOLECULAR SIMULATION